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- EMDB-70386: Zebrafish Abcb4 in IF-Narrow conformation in the presence of Elac... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-70386
TitleZebrafish Abcb4 in IF-Narrow conformation in the presence of Elacridar (ELA-IF-Narrow)
Map data
Sample
  • Complex: Zebrafish Abcb4 in inward-facing narrow-open conformation in the presence of Elacridar
    • Protein or peptide: ATP-binding cassette, sub-family B (MDR/TAP), member 4
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: elacridar
  • Ligand: CHOLIC ACID
KeywordsMultidrug resistance / Zebrafish Abcb4 / P-gp / Elacridar / TRANSPORT PROTEIN
Function / homology
Function and homology information


ABC-type protein transporter activity / toxin transmembrane transporter activity / ABC-type xenobiotic transporter / ABC-type xenobiotic transporter activity / ATPase-coupled transmembrane transporter activity / efflux transmembrane transporter activity / transmembrane transport / response to toxic substance / apical plasma membrane / ATP hydrolysis activity / ATP binding
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC-type xenobiotic transporter
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhan J / Xia D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Conformational Landscape of Zebrafish Abcb4
Authors: Zhan J / Xia D
History
DepositionApr 28, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70386.png

Downloads & links

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Map

FileDownload / File: emd_70386.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.21207538 - 0.52219105
Average (Standard dev.)0.00045716166 (±0.011693105)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_70386_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_70386_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Zebrafish Abcb4 in inward-facing narrow-open conformation in the ...

EntireName: Zebrafish Abcb4 in inward-facing narrow-open conformation in the presence of Elacridar
Components
  • Complex: Zebrafish Abcb4 in inward-facing narrow-open conformation in the presence of Elacridar
    • Protein or peptide: ATP-binding cassette, sub-family B (MDR/TAP), member 4
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: elacridar
  • Ligand: CHOLIC ACID

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Supramolecule #1: Zebrafish Abcb4 in inward-facing narrow-open conformation in the ...

SupramoleculeName: Zebrafish Abcb4 in inward-facing narrow-open conformation in the presence of Elacridar
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 140 KDa

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Macromolecule #1: ATP-binding cassette, sub-family B (MDR/TAP), member 4

MacromoleculeName: ATP-binding cassette, sub-family B (MDR/TAP), member 4
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Danio rerio (zebrafish)
Molecular weightTheoretical: 141.919781 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MGKKSKLKVS SDKKEENGDV SGEKNGKEEK EEKEKLEMVG PIELFRYADS IDILLMMLGL IMSMANGAVL PLMVIVFGDM TDSFVDDTL LDNLKNITLP PNFTFPETSN ITLGEKMTTH AIYYSIMGFV VLVAAYMQVA FWTLAAGRQV KKLRKIFFHS I MKQEIGWF ...String:
MGKKSKLKVS SDKKEENGDV SGEKNGKEEK EEKEKLEMVG PIELFRYADS IDILLMMLGL IMSMANGAVL PLMVIVFGDM TDSFVDDTL LDNLKNITLP PNFTFPETSN ITLGEKMTTH AIYYSIMGFV VLVAAYMQVA FWTLAAGRQV KKLRKIFFHS I MKQEIGWF DVNETGQLNT RLTDDVYKIN EGIGDKLGML IQNLTTFIVG IIIGFAKGWK LTLVILAVSP LLGISAAVIG KV MTTFTSK EQTAYAKAGA VAEEVLSSIR TVFAFGGQKK EIKRYHKNLE DAKNVGVRKA ITVNIAMGFT FFMIYMSYAL AFW YGSTLI LGGEYTIGML LTIFFAVLIG AFGLGQTSPN IQTFSSARGA AHKVFQIIDH EPKINSFSEE GYKLDVVKGN IEFK NIHFR YPSRDDVKVL NGMNLKVMSG QTIALVGSSG CGKSTTIQLL QRFYDPQEGS VSIDGHDIRS LNVRGLRELI GVVSQ EPVL FATTIAENIR YGRQDVTQDE IEQAAREANA YNFIMKLPDK FETLVGDRGT QMSGGQKQRI AIARALVRNP KILLLD EAT SALDAESETI VQAALDKVRL GRTTIVVAHR LSTIRNADVI AGFQNGEIVE LGTHDELMER KGIYHSLVNM QMFKSTE VA EEDSEEMTMD EKSPSVSSMN ERTLFRQKSR SGSEKELKEE EKPTEEEKVP NVSFLTVLKL NYPEWPYMVV GILCATIN G GMQPAFAVIF SKIIAVFAEP DQNLVRQRCD LYSLLFAGIG VLSFFTLFLQ GFCFGKAGEL LTMRLRFKAF NAMMRQDLA WYDDTKNSVG ALTTRLAADT AQVQGATGVR LATLAQNVAN LGTAIVISFV YGWQLTLLIL SIVPIMAVAG AIQMKLLAGH ALKDKKELE QAGKIATEAI ENVRTVVSLT RESKFESLYE ENLIVPYKNA KKKAHVFGLT FSFSQAMIYF AYAGCFKFGS W LIEQKLMT FEGVFLVISA VVYGAMAVGE ANSFTPNYAK AKMSASHVLM LINRAPAIDN SSEDGDKPDK FEGNVGFEHV YF KYPSRPD VPVLQGLKLR VKKGQTLALV GSSGCGKSTT IQLLERFYDP QQGRVMLDDN DAKQLNIHWL RSQIGIVSQE PVL FDCSLA ENIAYGDNSR EVDQEEIVEA AKAANIHSFI ENLPQRYQTQ AGDKGTQLSG GQKQRIAIAR AILRNPKVLL LDEA TSALD TESEKIVQDA LDKASKGRTC IIVAHRLSTI QNADCIAVVQ NGVVVEQGTH QQLLSQQGAY YTLVTSQMSH HHHHH H

UniProtKB: ABC-type xenobiotic transporter

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #4: elacridar

MacromoleculeName: elacridar / type: ligand / ID: 4 / Number of copies: 1 / Formula: R0Z
Molecular weightTheoretical: 563.643 Da
Chemical component information

ChemComp-R0Z:
elacridar

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Macromolecule #5: CHOLIC ACID

MacromoleculeName: CHOLIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: CHD
Molecular weightTheoretical: 408.571 Da
Chemical component information

ChemComp-CHD:
CHOLIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 478434
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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